Question: DESeq2 load failed for Bioconductor ver 3.9
0
gravatar for biancaineshoch
12 days ago by
biancaineshoch0 wrote:

Hello all.

I'm currently having issues loading DESeq2 into R version 3.6. I upgraded Bioconductor from version 3.7 to the latest version, 3.9. I am using my school's server to conduct RNA-Seq analysis.

Here is the error message that I receive:

> library(DESeq2)
Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘Hmisc’
In addition: Warning message:
replacing previous import ‘Biobase::dims’ by ‘BiocGenerics::dims’ when loading ‘DESeq2’

Here is the sessionInfo():

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] org.Hs.eg.db_3.8.2
 [2] PoiClaClu_1.0.2.1
 [3] RColorBrewer_1.1-2
 [4] pheatmap_1.0.12
 [5] GenomicAlignments_1.16.0
 [6] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.6
 [7] GenomicFeatures_1.36.0
 [8] AnnotationDbi_1.46.0
 [9] stringr_1.4.0
[10] stringi_1.4.3
[11] Rsamtools_1.32.3
[12] Biostrings_2.48.0
[13] XVector_0.20.0
[14] SummarizedExperiment_1.10.1
[15] DelayedArray_0.6.6
[16] BiocParallel_1.14.2
[17] matrixStats_0.54.0
[18] Biobase_2.40.0
[19] GenomicRanges_1.32.7
[20] GenomeInfoDb_1.20.0
[21] IRanges_2.14.12
[22] S4Vectors_0.18.3
[23] BiocGenerics_0.30.0

loaded via a namespace (and not attached):
 [1] progress_1.2.1         lattice_0.20-38        colorspace_1.4-1
 [4] rtracklayer_1.40.6     blob_1.1.1             XML_3.98-1.19
 [7] rlang_0.3.4            DBI_1.0.0              bit64_0.9-7
[10] GenomeInfoDbData_1.2.1 zlibbioc_1.26.0        munsell_0.5.0
[13] gtable_0.3.0           memoise_1.1.0          biomaRt_2.40.0
[16] Rcpp_1.0.1             xtable_1.8-4           scales_1.0.0
[19] BiocManager_1.30.4     annotate_1.62.0        bit_1.1-14
[22] hms_0.4.2              digest_0.6.18          grid_3.6.0
[25] tools_3.6.0            bitops_1.0-6           magrittr_1.5
[28] RCurl_1.95-4.12        RSQLite_2.1.1          crayon_1.3.4
[31] pkgconfig_2.0.2        Matrix_1.2-17          prettyunits_1.0.2
[34] assertthat_0.2.1       httr_1.4.0             R6_2.4.0
[37] compiler_3.6.0
deseq2 • 76 views
ADD COMMENTlink modified 12 days ago by Martin Morgan ♦♦ 23k • written 12 days ago by biancaineshoch0
Answer: DESeq2 load failed for Bioconductor ver 3.9
0
gravatar for Michael Love
12 days ago by
Michael Love23k
United States
Michael Love23k wrote:

DESeq2 depends on Hmisc, so that is the main problem here.

What happens when you try to install DESeq2:

BiocManager::install("DESeq2")

If you do not have permissions, you may have to ask an administrator to reinstall for you.

ADD COMMENTlink written 12 days ago by Michael Love23k

Thank you for your quick reply! My PI has root access and got a similar error, so I'm not sure my problem is permissions. The entire output stream is too long for me to include, so I cut to the first fatal error. Here is the result of installing DESeq2:

> > BiocManager::install("DESeq2") Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'DESeq2' also installing the dependencies ‘vctrs’, ‘pillar’, ‘tibble’, ‘viridis’,
> ‘ggplot2’, ‘Hmisc’ trying URL
> 'https://cloud.r-project.org/src/contrib/vctrs_0.1.0.tar.gz' Content
> type 'application/x-gzip' length 412633 bytes (402 KB)
> ================================================== downloaded 402 KB trying URL
> 'https://cloud.r-project.org/src/contrib/Hmisc_4.2-0.tar.gz' Content
> type 'application/x-gzip' length 732731 bytes (715 KB)
> ================================================== downloaded 715 KB trying URL
> 'https://bioconductor.org/packages/3.9/bioc/src/contrib/DESeq2_1.24.0.tar.gz'
> Content type 'application/x-gzip' length 2056901 bytes (2.0 MB)
> ================================================== downloaded 2.0 MB
> * installing *source* package ‘vctrs’ ...
> ** package ‘vctrs’ successfully unpacked and MD5 sums checked
> ** using staged installation
> ** libs gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c compare.c -o compare.o In file included from vctrs.h:2:0,
>                  from compare.c:1: /usr/share/R/include/R.h:55:80: fatal error: stdlib.h: No such file or directory compilation
> terminated. /usr/lib/R/etc/Makeconf:167: recipe for target 'compare.o'
> failed make: *** [compare.o] Error 1 ERROR: compilation failed for
> package ‘vctrs’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/vctrs’ ERROR: dependency ‘vctrs’ is not available for package ‘pillar’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/pillar’ ERROR: dependency ‘pillar’ is not available for package ‘tibble’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/tibble’ ERROR: dependency ‘tibble’ is not available for package ‘ggplot2’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/ggplot2’ ERROR: dependency ‘ggplot2’ is not available for package ‘viridis’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/viridis’ ERROR: dependencies ‘ggplot2’, ‘viridis’ are not available for package
> ‘Hmisc’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/Hmisc’ ERROR: dependencies ‘ggplot2’, ‘Hmisc’ are not available for package ‘DESeq2’
> * removing ‘/home/bih1/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’ The downloaded source packages are in
>         ‘/tmp/RtmpfDJ5u3/downloaded_packages’ installation path not writeable, unable to update packages: acepack, ade4,   affy, affyio,
> askpass, backports, base64enc, bdsmatrix, bibtex, bindrcpp,   Biobase,
> BiocParallel, Biostrings, bit, bit64, bitops, car, caTools,  
> checkmate, colorspace, covr, curl, data.table, DelayedArray, deldir,
> diffobj,   digest, ellipsis, fansi, fastmatch, FNN, freetypeharfbuzz,
> fs, gdtools, gee,   GenomicAlignments, GenomicRanges, git2r, glue,
> kernlab, ks, later, lazyeval, leaps,   openxlsx, pcaMethods, pkgload,
> plyr, png, polysat, preprocessCore, pROC,   reshape2, reticulate, rgl,
> rlang, Rmpi, RSQLite, rtracklayer, Rwave,   SummarizedExperiment,
> edgeR, effects, expm, irlba, lme4, lmtest, locfit, maptools,  
> foreign, genefilter, GOstats, graph, gss, KernSmooth, lattice, MASS,
> Matrix,   RcppParallel, Rgraphviz, rmutil, spatial, stable, statip,
> survival, sva 

> Warning messages: 1: In install.packages(pkgs = doing,
> lib = lib, repos = repos, ...) :   installation of package ‘vctrs’ had
> non-zero exit status 2: In install.packages(pkgs = doing, lib = lib,
> repos = repos, ...) :   installation of package ‘pillar’ had non-zero
> exit status 3: In install.packages(pkgs = doing, lib = lib, repos =
> repos, ...) :   installation of package ‘tibble’ had non-zero exit
> status 4: In install.packages(pkgs = doing, lib = lib, repos = repos,
> ...) :   installation of package ‘ggplot2’ had non-zero exit status 5:
> In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :  
> installation of package ‘viridis’ had non-zero exit status 6: In
> install.packages(pkgs = doing, lib = lib, repos = repos, ...) :  
> installation of package ‘Hmisc’ had non-zero exit status 7: In
> install.packages(pkgs = doing, lib = lib, repos = repos, ...) :  
> installation of package ‘DESeq2’ had non-zero exit status
ADD REPLYlink modified 12 days ago • written 12 days ago by biancaineshoch0

Looks like the problem starts with vctrs:

fatal error: stdlib.h: No such file or directory compilation terminated. /usr/lib/R/etc/Makeconf:167: recipe for target 'compare.o' failed make: * [compare.o] Error 1 ERROR: compilation failed for package ‘vctrs’

Not sure how you could fix on your system...

DESeq2 install fine on Ubuntu for many users I know (myself included).

ADD REPLYlink written 12 days ago by Michael Love23k

Hmm. I'll continue to troubleshoot then. Thanks for your help, I'm a big fan of your work.

ADD REPLYlink written 12 days ago by biancaineshoch0

Hmm. I'll continue to troubleshoot then. Thanks for your help, I'm a big fan of your work.

ADD REPLYlink written 12 days ago by biancaineshoch0

My guess is that you have updated your OS or compilers after installing R, and the best bet would be to re-install R. Also simplify the problem to tackling the first failure -- BiocManager::install("vctrs")

ADD REPLYlink written 12 days ago by Martin Morgan ♦♦ 23k
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